This may be a silly question, but I'm looking to pick Skyrim back up and do some modding. Before I do, I was wondering if there are any compatibility issues between the different versions of Skryim / DLCS - the downloadable from Steam, the disc installed PC version, and the Legendary Edition. Is there any edition best for modding? Any difference at all?

There's no difference whatsoever. Each version is no different from the Steam version. In order to use any of them, they need to be associated with Steam. Legendary is just Skyrim + DLCs. Disc version is just Skyrim on disc. There is no difference between any of them with Skyrim + DLCs.

Like deaths_soul stated no difference so it is just a matter of which happens to be cheaper for you to get. Likely the Legendary Edition will be the better deal if you want all the DLC's and need the game as well.

As long as your game is patched up to version 1.9.32, you should be fine.